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Blanco-Melo, D., Campbell, M. A., Zhu, H., Dennis, T. P., Modha, S. , Lytras, S., Hughes, J. , Gatseva, A. and Gifford, R. J. (2024) A novel approach to exploring the dark genome and its application to mapping of the vertebrate virus fossil record. Genome Biology, 25(1), 120. (doi: 10.1186/s13059-024-03258-y) (PMID:38741126) (PMCID:PMC11089739)
Wang, C. et al. (2023) MalariaSED: a deep learning framework to decipher the regulatory contributions of noncoding variants in malaria parasites. Genome Biology, 24(1), 231. (doi: 10.1186/s13059-023-03063-z) (PMID:37845769) (PMCID:PMC10577899)
Gillen, S. L., Giacomelli, C., Hodge, K., Zanivan, S. , Bushell, M. and Wilczynska, A. (2021) Differential regulation of mRNA fate by the human Ccr4-Not complex is driven by coding sequence composition and mRNA localization. Genome Biology, 22, 284. (doi: 10.1186/s13059-021-02494-w) (PMID:34615539) (PMCID:PMC8496106)
Waldron, J. A., Tack, D. C., Ritchey, L. E., Gillen, S. L., Wilczynska, A., Turro, E., Bevilacqua, P. C., Assmann, S. M., Bushell, M. and Le Quesne, J. (2019) mRNA structural elements immediately upstream of the start codon dictate dependence upon eIF4A helicase activity. Genome Biology, 20(1), 300. (doi: 10.1186/s13059-019-1901-2) (PMID:31888698) (PMCID:PMC6936103)
Wilczynska, A. et al. (2019) eIF4A2 drives repression of translation at initiation by Ccr4-Not through purine-rich motifs in the 5’UTR. Genome Biology, 20, 262. (doi: 10.1186/s13059-019-1857-2) (PMID:31791371) (PMCID:PMC6886185)
Prins, B. P. et al. (2018) Exome-chip meta-analysis identifies novel loci associated with cardiac conduction, including ADAMTS6. Genome Biology, 19, 87. (doi: 10.1186/s13059-018-1457-6) (PMID:30012220) (PMCID:PMC6048820)
Quince, C., Delmont, T. O., Raguideau, S., Alneberg, J., Darling, A. E., Collins, G. and Eren, A. M. (2017) DESMAN: a new tool for de novo extraction of strains from metagenomes. Genome Biology, 18, 181. (doi: 10.1186/s13059-017-1309-9) (PMID:28934976) (PMCID:PMC5607848)
Cole, J. J. et al. (2017) Diverse interventions that extend mouse lifespan suppress shared age-associated epigenetic changes at critical gene regulatory regions. Genome Biology, 18, 58. (doi: 10.1186/s13059-017-1185-3) (PMID:28351383) (PMCID:PMC5370462)
Wang, T., Tsui, B., Kreisberg, J. F., Robertson, N. A., Gross, A. M., Yu, M. K., Carter, H., Brown-Borg, H. M., Adams, P. D. and Ideker, T. (2017) Epigenetic aging signatures in mice livers are slowed by dwarfism, calorie restriction and rapamycin treatment. Genome Biology, 18, 57. (doi: 10.1186/s13059-017-1186-2) (PMID:28351423) (PMCID:PMC5371228)
de Santiago, I., Liu, W., Yuan, K. , O'Reilly, M., Chilamakuri, C. S. R., Ponder, B. A.J., Meyer, K. B. and Markowetz, F. (2017) BaalChIP: Bayesian analysis of allele-specific transcription factor binding in cancer genomes. Genome Biology, 18, 39. (doi: 10.1186/s13059-017-1165-7) (PMID:28235418) (PMCID:PMC5326502)
Jiang, Y. et al. (2016) An expanded evaluation of protein function prediction methods shows an improvement in accuracy. Genome Biology, 17, 184. (doi: 10.1186/s13059-016-1037-6) (PMID:27604469) (PMCID:PMC5015320)
Nelson, D. M. et al. (2016) Mapping H4K20me3 onto the chromatin landscape of senescent cells indicates a function in control of cell senescence and tumor suppression through preservation of genetic and epigenetic stability. Genome Biology, 17, 158. (doi: 10.1186/s13059-016-1017-x) (PMID:27457071) (PMCID:PMC4960804)
Eves-van den Akker, S. et al. (2016) The genome of the yellow potato cyst nematode, Globodera rostochiensis, reveals insights into the basis of parasitism and virulence. Genome Biology, 17, 124. (doi: 10.1186/s13059-016-0985-1) (PMID:27286965) (PMCID:PMC4901422)
Hunt, M., Silva, N. D., Otto, T. D. , Parkhill, J., Keane, J. A. and Harris, S. R. (2015) Circlator: automated circularization of genome assemblies using long sequencing reads. Genome Biology, 16, 294. (doi: 10.1186/s13059-015-0849-0) (PMID:26714481) (PMCID:PMC4699355)
Barrass, J. D., Reid, J. E.A., Huang, Y., Hector, R. D. , Sanguinetti, G., Beggs, J. D. and Granneman, S. (2015) Transcriptome-wide RNA processing kinetics revealed using extremely short 4tU labeling. Genome Biology, 16, 282. (doi: 10.1186/s13059-015-0848-1) (PMID:26679539) (PMCID:PMC4699367)
Marques, C. A. , Dickens, N. J. , Paape, D. , Campbell, S. J. and McCulloch, R. (2015) Genome-wide mapping reveals single-origin chromosome replication in Leishmania, a eukaryotic microbe. Genome Biology, 16, 230. (doi: 10.1186/s13059-015-0788-9) (PMID:26481451) (PMCID:PMC4612428)
Yuan, K. , Sakoparnig, T., Markowetz, F. and Beerenwinkel, N. (2015) BitPhylogeny: a probabilistic framework for reconstructing intra-tumor phylogenies. Genome Biology, 16(1), p. 36. (doi: 10.1186/s13059-015-0592-6) (PMID:25786108) (PMCID:PMC4359483)
Lizio, M. et al. (2015) Gateways to the FANTOM5 promoter level mammalian expression atlas. Genome Biology, 16, 22. (doi: 10.1186/s13059-014-0560-6) (PMID:25723102) (PMCID:PMC4310165)
Lund, K., Cole, J., VanderKraats, N. D., McBryan, T., Pchelintsev, N. A., Clark, W., Copland, M. , Edwards, J. R. and Adams, P. (2014) DNMT inhibitors reverse a specific signature of aberrant promoter DNA methylation and associated gene silencing in AML. Genome Biology, 15(7), p. 406. (doi: 10.1186/s13059-014-0406-2)
Hunt, M., Newbold, C., Berriman, M. and Otto, T. D. (2014) A comprehensive evaluation of assembly scaffolding tools. Genome Biology, 15(3), R42. (doi: 10.1186/gb-2014-15-3-r42) (PMID:24581555) (PMCID:PMC4053845)
Cotton, J. A. et al. (2014) The genome and life-stage specific transcriptomes of Globodera pallida elucidate key aspects of plant parasitism by a cyst nematode. Genome Biology, 15(3), R43. (doi: 10.1186/gb-2014-15-3-r43) (PMID:24580726) (PMCID:PMC4054857)
Martin, H. C., Wani, S., Steptoe, A. L., Krishnan, K., Nones, K., Nourbakhsh, E., Vlassov, A., Grimmond, S. M. and Cloonan, N. (2014) Imperfect centered miRNA binding sites are common and can mediate repression of target mRNAs. Genome Biology, 15(3), R51. (doi: 10.1186/gb-2014-15-3-r51) (PMID:24629056)
Webb, S., Hector, R. D. , Kudla, G. and Granneman, S. (2014) PAR-CLIP data indicate that Nrd1-Nab3-dependent transcription termination regulates expression of hundreds of protein coding genes in yeast. Genome Biology, 15(1), R8. (doi: 10.1186/gb-2014-15-1-r8)
Laing, R. et al. (2013) The genome and transcriptome of haemonchus contortus, a key model parasite for drug and vaccine discovery. Genome Biology, 14(8), R88. (doi: 10.1186/gb-2013-14-8-r88) (PMID:23985316) (PMCID:PMC4054779)
Hunt, M., Kikuchi, T., Sanders, M., Newbold, C., Berriman, M. and Otto, T. D. (2013) REAPR: a universal tool for genome assembly evaluation. Genome Biology, 14(5), R47. (doi: 10.1186/gb-2013-14-5-r47) (PMID:22678431) (PMCID:PMC3648784)
Fischer, A., Illingworth, C. J.R. , Campbell, P. J. and Mustonen, V. (2013) EMu: probabilistic inference of mutational processes and their localization in the cancer genome. Genome Biology, 14(4), R39. (doi: 10.1186/gb-2013-14-4-r39) (PMID:23628380) (PMCID:PMC3663107)
Sani, E., Herzyk, P. , Perrella, G., Colot, V. and Amtmann, A. (2013) Hyperosmotic priming of arabidopsis seedlings establishes a long-term somatic memory accompanied by specific changes of the epigenome. Genome Biology, 14(6), R59. (doi: 10.1186/gb-2013-14-6-r59) (PMID:23767915) (PMCID:PMC3707022)
Solana, J., Kao, D., Mihaylova, Y., Jaber-Hijazi, F. , Malla, S., Wilson, R. and Aboobaker, A. (2012) Defining the molecular profile of planarian pluripotent stem cells using a combinatorial RNA-seq, RNA interference and irradiation approach. Genome Biology, 13(3), R19. (doi: 10.1186/gb-2012-13-3-r19) (PMID:22439894) (PMCID:PMC3439970)
Donati, C. et al. (2010) Structure and dynamics of the pan-genome of Streptococcus pneumoniae and closely related species. Genome Biology, 11(10), R107--. (doi: 10.1186/gb-2010-11-10-r107)
Tsai, I. J., Otto, T. D. and Berriman, M. (2010) Improving draft assemblies by iterative mapping and assembly of short reads to eliminate gaps. Genome Biology, 11, R41. (doi: 10.1186/gb-2010-11-4-r41) (PMID:20388197) (PMCID:PMC2884544)
Tait, A. (2009) Genetics and genomics converge on the human blood fluke. Genome Biology, 10(6), p. 225. (doi: 10.1186/gb-2009-10-6-225)
Cooper, A. , Tait, A., Sweeney, L., Tweedie, A., Morrison, L., Turner, C.M.R. and MacLeod, A. (2008) Genetic analysis of the human infective trypanosome Trypanosoma brucei gambiense: chromosomal segregation, crossing over, and the construction of a genetic map. Genome Biology, 9(6), R103. (doi: 10.1186/gb-2008-9-6-r103)
Carter, S. and Vousden, K. (2008) A role for Numb in p53 stabilization. Genome Biology, 9(5), p. 221. (doi: 10.1186/gb-2008-9-5-221)
Zanivan, S. , Cascone, I., Peyron, C., Molineris, I., Marchio, S., Caselle, M. and Bussolino, F. (2007) A new computational approach to analyze human protein complexes and predict novel protein interactions. Genome Biology, 8, R256. (doi: 10.1186/gb-2007-8-12-r256) (PMID:18053208) (PMCID:PMC2246258)
Hakes, L., Pinney, J. W., Lovell, S. C., Oliver, S. G. and Robertson, D. L. (2007) All duplicates are not equal: the difference between small-scale and genome duplication. Genome Biology, 8(10), R209. (doi: 10.1186/gb-2007-8-10-r209) (PMID:17916239) (PMCID:PMC2246283)
McElwee, J.J. et al. (2007) Evolutionary conservation of regulated longevity assurance mechanisms. Genome Biology, 8(7), R132. (doi: 10.1186/gb-2007-8-7-r132)
Sargeant, T. J., Marti, M. , Caler, E., Carlton, J. M., Simpson, K., Speed, T. P. and Cowman, A. F. (2006) Lineage-specific expansion of proteins exported to erythrocytes in malaria parasites. Genome Biology, 7(2), R12. (doi: 10.1186/gb-2006-7-2-r12) (PMID:16507167) (PMCID:PMC1431722)
Barkess, G. (2006) Chromatin remodeling and genome stability. Genome Biology, 7, 319. (doi: 10.1186/gb-2006-7-6-319) (PMID:16817945) (PMCID:PMC1779531)
Wilkins, A., Szafranski, K., Fraser, D. J., Bakthavatsalam, D., Müller, R., Fisher, P. R., Glöckner, G., Eichinger, L., Noegel, A. A. and Insall, R. H. (2005) The Dictyostelium genome encodes numerous RasGEFs with multiple biological roles. Genome Biology, 6(8), R68. (doi: 10.1186/gb-2005-6-8-r68) (PMID:16086850) (PMCID:PMC1273635)
Insall, R. (2005) The Dictyostelium genome: the private life of a social model revealed? Genome Biology, 6(6), 222. (doi: 10.1186/gb-2005-6-6-222) (PMID:15960812) (PMCID:PMC1175964)
Dow, J. (2005) Physiology engages with functional genomics - at last. Genome Biology, 6(8), pp. 3351-3353. (doi: 10.1186/gb-2005-6-8-335) (PMID:16086845) (PMCID:PMC1273626)
Wang, J., Kean, L., Yang, J., Allan, A., Davies, S., Herzyk, P. and Dow, J. (2004) Function-informed transcriptome analysis of Drosophila renal tubule. Genome Biology, 5, (PMID:15345053) (PMCID:PMC522876)
Dickens, N.J. and Ponting, C.P. (2003) THoR: a tool for domain discovery and curation of multiple alignments. Genome Biology, 4(8), R52. (doi: 10.1186/gb-2003-4-8-r52) (PMID:12914660) (PMCID:PMC193644)
Dixon, D. P., Lapthorn, A. and Edwards, R. (2002) Plant glutathione transferases. Genome Biology, 3(3), reviews300. (doi: 10.1186/gb-2002-3-3-reviews3004) (PMID:11897031) (PMCID:PMC139027)
Cotton, J. (2001) Homologous recombination in animal mitochondria. Genome Biology, 2(10), reports0034. (doi: 10.1186/gb-2001-2-10-reports0034)
Cotton, J. (2001) A new profusion of planktonic eukaryotes. Genome Biology, 2(7), reports0016. (doi: 10.1186/gb-2001-2-7-reports0016)
Cotton, J. (2001) Retroviruses from retrotransposons. Genome Biology, 2(2), reports0006. (doi: 10.1186/gb-2001-2-2-reports0006)
Ponting, C.P. and Dickens, N.J. (2001) Genome cartography through domain annotation. Genome Biology, 2(7), Comment 2006.